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Merge branch 'feature-scatter_annotation' into 'develop'
Added scattering on annotation Fixes #305 and #324 See merge request !374
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- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala 135 additions, 134 deletions.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
- biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala 7 additions, 2 deletions...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala 4 additions, 3 deletions...src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
- biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala 29 additions, 19 deletions.../main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala 20 additions, 6 deletions...s/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
- biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala 7 additions, 0 deletions...s/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
- shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala 1 addition, 1 deletion...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
- toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala 83 additions, 25 deletions...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
- toucan/src/test/resources/chrQ2.vcf.gz 0 additions, 0 deletionstoucan/src/test/resources/chrQ2.vcf.gz
- toucan/src/test/resources/fake_chrQ.dict 2 additions, 0 deletionstoucan/src/test/resources/fake_chrQ.dict
- toucan/src/test/resources/fake_chrQ.fa 2 additions, 0 deletionstoucan/src/test/resources/fake_chrQ.fa
- toucan/src/test/resources/fake_chrQ.fa.fai 1 addition, 0 deletionstoucan/src/test/resources/fake_chrQ.fa.fai
- toucan/src/test/resources/log4j.properties 25 additions, 0 deletionstoucan/src/test/resources/log4j.properties
- toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala 111 additions, 0 deletions...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
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